rs2061579

chr12-74544475-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001136262.2(ATXN7L3B):c.*6069A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 151,810 control chromosomes in the GnomAD database, including 6,187 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.26 (6187 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ATXN7L3B NM_001136262.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.464

Genes affected

ATXN7L3B (HGNC:37931): (ataxin 7 like 3B) Involved in regulation of gene expression. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATXN7L3B	NM_001136262.2	c.*6069A>G		3_prime_UTR_variant	1/1	ENST00000519948.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATXN7L3B	ENST00000519948.4	c.*6069A>G		3_prime_UTR_variant	1/1		NM_001136262.2	P1

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39450 AN: 151692 Hom.: 6179 Cov.: 32

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.0918

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.250

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.260 AC: 39494 AN: 151810 Hom.: 6187 Cov.: 32 AF XY: 0.253 AC XY: 18754 AN XY: 74208

Gnomad4 AFR AF: 0.438

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.264

Gnomad4 EAS AF: 0.0916

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.247

Alfa AF: 0.223 Hom.: 1961

Bravo AF: 0.272

Asia WGS AF: 0.145 AC: 508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.60
Dann	Benign	0.22

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2061579; hg19: chr12-74938255;